Informed training set design enables efficient machine learning-assisted directed protein evolution

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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

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Deep Dive into Machine Learning Models for Protein Engineering

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TLmutation: Predicting the Effects of Mutations Using Transfer Learning

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Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations

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Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

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Predicting Splicing from Primary Sequence with Deep Learning

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Computational Complexity as an Ultimate Constraint on Evolution

(2019) Artem Kaznatcheev   GENETICS

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Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis

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Machine Learning in Enzyme Engineering

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Recent Trends in Deep Learning Based Natural Language Processing [Review Article]

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Clustering huge protein sequence sets in linear time

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Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

The EVcouplings Python framework for coevolutionary sequence analysis

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UniProt: a worldwide hub of protein knowledge

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Insurance Premium Prediction via Gradient Tree-Boosted Tweedie Compound Poisson Models

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Deep Convolutional Neural Networks for Image Classification: A Comprehensive Review

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Local fitness landscape of the green fluorescent protein

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Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

How mutational epistasis impairs predictability in protein evolution and design

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Adaptation in protein fitness landscapes is facilitated by indirect paths

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ProFET: Feature engineering captures high-level protein functions

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AB-Bind: Antibody binding mutational database for computational affinity predictions

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A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

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A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

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Navigating the protein fitness landscape with Gaussian processes

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Capturing the mutational landscape of the beta-lactamase TEM-1

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Interpretable Numerical Descriptors of Amino Acid Space

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Exploring protein fitness landscapes by directed evolution

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